BLAST plus: architecture and applications. BMC Bioinformatics. 2009;10:421. Article PubMed PubMed Central Google Scholar Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb). 2021;2:100141. ...
Our evaluation covered three key perspectives: (1) spatial domain detection on single-cell spatial transcriptomics data, (2) spatial domain detection on spot resolution spatial transcriptomics data, and (3) TLS-like domain detection. For the first test (Fig. 2a), we can see that SpaDo ...
For each putative site, we sorted the pool of BLAST hits by subject strand (in this case, “subject” refers to our plant reference genome) to find which of the paired reads were associated with either the plus or minus strand. Because the transgene-containing end of the amplicon is closes...
Phytophthora root rot caused by the oomycete Phytophthora capsici is the most devastating disease in pepper production worldwide, and current management strategies have not been effective in preventing this disease. Therefore, the use of resistant variet
All potential genes were classified by BLAST using the KEGG database (v2.7.1) [74]. Statistical analysis The content of nine monosaccharides were expressed as mean ± SD. One-way anOVA (ANOVA) was used to analyze differences in content of total polysaccharides between groups and the ...
While some previous methods also align to the virus first [97], either the software no longer appears available where specified at publication [98, 99], or they use BLAST [100, 101] instead of a faster short read aligner [102]. Unlike ViFi [58], Polyidus requires that the chimera ...
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Fig. 3 Map of central metabolic pathways inR. toruloidesBOT-A2. Pathways were reconstructed from genome and RNAseq data, using KEGG, SGD and BLASTp. The network includes glycolysis (pink), the pentose phosphate pathway (blue), the TCA cycle (pale yellow), lipid biosynthesis, triacylglycerol bi...
Global p-values were calculated based on 1000 permutations of the original data using a BLAST-like search algorithm [28]. Purifying selection tests and Ps,PN calculation Analyses were conducted using MEGA v.3.1 [53]. Pairwise dN/dS ratios and significance values were calculated using the Nei-...
Functional enrichment using gene ontology terms and Fisher's Exact Test was performed using Blast2GO for the sets of up-regulated unigenes in each of the three tissues (bean, leaf and flower). The full set of unigenes of the PUCE CAFE array was used as the reference set. The resulting ...